Dr. Dagmar Woebken

Group Leader
University of Vienna
Division of Microbial Ecology
Althanstr. 14
A-1090 Vienna
Phone: +43 1 4277 76613

Main areas of research                           

My research interests can be defined in the fields of microbial ecology, nutrient/element cycling, the global nitrogen (N)-cycle and particularly the process N2 fixation therein, terrestrial ecosystems and structured ecosystems such as microbial mats and biological soil crusts. My long-term goal is to identify the active participants in key processes within the carbon (C)- and N-cycle, the factors that regulate and govern their activities, the trophic interactions among microorganisms, but also between plants and microorganisms within an ecosystem, and the interdependence of C- and N-cycle in terrestrial ecosystems.

Method development. The research in my group at the University of Vienna focuses on the active microbial participants involved in the N- and C-cycle across terrestrial ecosystems, microbial mats and biological soil crusts. To reach this goal, we use a multidisciplinary approach combining activity measurements on the process-level, analysis of the genetic potential on the community-level (functional gene and transcript sequencing) and confirmation of the targeted activity on the single-cell level by SIP and high-resolution secondary ion mass spectrometry (NanoSIMS). Single-cell based approaches such as NanoSIMS and Raman microspectroscopy are increasingly applied in microbial ecology studies. Raman microspectroscopy and NanoSIMS are techniques that permit the analysis of microbiological samples down to the single-cell level. These powerful techniques have recently helped define the field of single-cell ecophysiology especially when combined with stable isotope tracers (such as 13C, 15N and D2O) and/or identification of the targeted cell using fluorescence in situ hybridization (FISH). To that end, we are developing and optimizing methods to perform these in situ single-cell analyses in complex ecosystems, such as soils.

Some of these developments have been highlighted by the Joint Genome Institute, Science Highlights: A Single-Cell Pipeline for Soil Samples.

Diazotrophy. We are investigating the active N2-fixing community (diazotrophs) in soils along with the factors that govern their activity such as the energy sources available for this highly energy-costly process. This project also encompasses biological soil crusts, where autotrophically fixed CO2 will be the major source of C for N fixation. We are using the multidisciplinary approach that was used when I previously identified the active microbial community members in two photosynthetic microbial mats, Elkhorn Slough, California, USA  and Guerrero Negro, Mexico. We have extended our on-going diazotrophy studies to the investigation of diazotrophs associated with plant roots. Plants excrete C compounds into the rhizosphere, which can be utilized by the microorganism inhabiting this niche as a source of energy. Therefore, this represents a niche particularly suited for bacteria that fix N2 and have a high need of energy. Both systems, biological soil crusts and the rhizosphere, are prime examples of the linkage of the N- and C-cycle in terrestrial systems that I am particularly interested in.

Microbial cellulose degradation. In addition to the N-cycle, we are currently investigating the active participants as well as edaphic drivers and limitations of microbial cellulose degradation. Soils contain the largest pool of carbon (C) on Earth with cellulose being the most abundant polymer, as it is a key component of plant structural C. Members of the Bacteria and Fungi are responsible for degrading cellulose, but their contributions remain unresolved. For a better understanding of the terrestrial C cycle it is vital to elucidate the active participants in cellulose degradation and identify different niches of cellulose-responsive guilds. We are combing stable isotope probing with next generation sequencing to characterize cellulose-responsive guilds across various amendments, along with single-cell based approaches to appreciate this process at a more relevant spatial scale.

Microaerophiles. We recently started a project that focuses on a ubiquitous group of microorganisms in soils, members of the phylum Acidobacteria. In this project, we will also investigate the activity of microorganisms under microoxic conditions in terrestrial ecosystems. Evidence exists that most of microbial activity in natural habitats is actually not performed under atmospheric but under reduced O2 levels. The diversity of microorganisms with the capacity to make a living under reduced O2 concentrations is not well understood and will be particularly investigated in terrestrial ecosystems in this project.

Microbial dormancy. Soils are considered the last scientific frontiers that harbor one of the most diverse microbial communities on Earth. It is hypothesized that this diversity allows for redundancy in microbial key processes, thereby ensuring ecosystem stability. Much of this functional redundancy is embodied in non-active, dormant microorganisms that represent the ‘microbial seed bank’. It is hypothesized that dormant microorganisms can be recruited to participate in a given function upon resuscitation with environmental cue(s). In this project I will test this hypothesis on a level that matters for ecosystem processes – the functional level – by an innovative approach combining stable isotope probing (SIP) and sequencing with process-level and single-cell activity analysis.

Current Research projects


  • Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D. (in press) Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol
  • Angel R, Panhölzl C, Gabriel R, Herbold C, Wanek W, Richter A, Eichorst SA, Woebken D. (in press) Application of stable-isotope labelling techniques for the detection of active diazotrophs. Environ Microbiol. DOI: 10.1111/1462-2920.13954.
  • Eichorst SA, Trojan D, Woebken D. 2017. Genus Terriglobus. In Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Chichester, England. 
  • Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D. 2015. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol. Ecol. DOI: http://dx.doi.org/10.1093/femsec/fiv106 fiv106.
  • Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, López Cortés A, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. 2015. Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J. 9:485-496.
  • Berry D, Mader E, Lee TK, Woebken D, Wang Y, Zhu D, Palatinszky M, Schintlmeister A, Schmid MC, Hanson BT, Shterzer N, Mizrahi I, Rauch I, Decker T, Bocklitz T, Popp J, Gibson CM, Fowler PW, Huang WE, Wagner M. 2015. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. PNAS 112: E194-203.
  • Eichorst, SA and Woebken, D. 2014. Investigation of microorganisms at the single-cell level using Raman Microspectroscopy and Nanometer-scale Secondary Ion Mass Spectrometry. In: Skovhus TL, Caffrey S, editors. Molecular Methods and Applications in MIcrobiology. Norfolk, UK: Caister Academic Press; p 203-211.
  • Burow LC, Woebken D, Bebout BM, Marshall IPG, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM. 2014. Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community. Geobiology 12: 221–230.
  • Burow LC*, Woebken D*, Marshall IPG, Lindquist EA, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe SG, Pett-Ridge J, Weber PK, Spormann AM, Singer SW. 2013. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS. ISME J. 7:817-829. (*co-first authors)
  • Woebken D, Burow LC, Prufert-Bebout L, Bebout BM, Hoehler TM, Pett-Ridge J, Singer SW§, Spormann AM, Weber PK. 2012. Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. ISME J. 6:1427-1439
  • Burow LC, Woebken D, Bebout BM , McMurdie PJ , Singer SW , Pett-Ridge J , Prufert-Bebout L, Spormann AM , Weber PK, Hoehler TM. 2012. Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J. 6:863–874

The Woebken GROUP

Joining the team

Information on open research positions can be found here or can be obtained by contacting Dagmar. If you are interested in joining our team with your own fellowship, please check out our PhD & postdoc program.


Uni Wien forscht: Mikrobiologin Dagmar Wöbken auf Spurensuche (2014)

Im Reich der wichtigen Kleinen (2014)

University of Vienna, KinderUni (2014, 2015, 2016, 2017)
Summer Workshop entitled "What would the world look like without microbes?". Course description: Microbes are all around us and are very important. Imagine what the world would look like without them? Come spend some time at our Microbe Exhibition and learn more. We will explore what microbes do in nature, for instance in dirt and in lakes, how they help us make food, and how they help plants to grow.
    3-day workshop for school children entitled "An Underground Adventure. Dirt - The Scoop on Soil". This 3-day workshop was a synthesis of presentations, discussions and hand-on activities designed to develop an awareness and appreciation for soil and soil microorganisms. The themes covered topics such as "What is Soil?", "What lives in soil?", and what we can do to save/preserve the soil, jobs with soil and a question-and-answer session with the students.